mygaussfit.m

function [sigma,mu,A]=mygaussfit(x,y,h)
% Copyright (c) 2007, Yohanan Sivan
% All rights reserved.
% 
% Redistribution and use in source and binary forms, with or without 
% modification, are permitted provided that the following conditions are 
% met:
% 
%     * Redistributions of source code must retain the above copyright 
%       notice, this list of conditions and the following disclaimer.
%     * Redistributions in binary form must reproduce the above copyright 
%       notice, this list of conditions and the following disclaimer in 
%       the documentation and/or other materials provided with the distribution
%       
% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE 
% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
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% SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
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% from http://www.mathworks.com/matlabcentral/fileexchange/11733
%modified SAR to just get rid of zeros

% [sigma,mu,A]=mygaussfit(x,y)
% [sigma,mu,A]=mygaussfit(x,y,h)
%
% this function is doing fit to the function
% y=A * exp( -(x-mu)^2 / (2*sigma^2) )
%
% the fitting is been done by a polyfit
% the lan of the data.
%
% h is the threshold which is the fraction
% from the maximum y height that the data
% is been taken from.
% h should be a number between 0-1.
% if h have not been taken it is set to be 0.2
% as default.
%


%% threshold
if nargin==2, h=0.2;

%% cutting 
ymax=max(y);
xnew=[];
ynew=[];
for n=1:length(x)
    if y(n)>ymax*h;
        xnew=[xnew,x(n)];
        ynew=[ynew,y(n)];
    end;
end;
end;

%just get rid of 0s
ab0=find(y>0);
xnew=x(ab0);
ynew=y(ab0);
%% fitting
ylog=log(ynew);
xlog=xnew;
p=polyfit(xlog,ylog,2);
A2=p(1);
A1=p(2);
A0=p(3);
sigma=sqrt(-1/(2*A2));
mu=A1*sigma^2;
A=exp(A0+mu^2/(2*sigma^2));